Genome sequencing technologies have begun a revolution in the diagnosis of human diseases, and infections, and in the characterization of microbes. Specific mutations linked to cancer, metabolic disorders, as well as bacterial and viral drug resistance are often as small as a single nucleotide polymorphism (SNP). Unfortunately, DNA microarrays and the current generation of nucleic acid-amplification based techniques under development for the detection of SNPs and other genetic polymorphisms are technically complex and expensive. These factors are likely to limit the widespread availability of genetic testing. We have pioneered a simple, rapid, and robust method for DNA sequence identification and SNP analysis that uses new types of fluorescent probes called molecular beacons. Molecular beacons can be used to develop highly accurate and inexpensive polymerase chain reaction (PCR) assays, but these assays have been limited by the requirement for costly and complex detection instruments. Molecular beacons are ideally suited for use in assays that take maximum advantage of advances in polymer microfabrication technology, cooled CCD imaging systems, ink jet directed microprinting, and advanced image processing software modules. This proposal will develop inexpensive desktop systems and assays for genetic diagnosis and SNP detection. It will concentrate on developing urgently needed assays to simultaneously diagnose Mycobacterium tuberculosis, and detect drug resistance directly from clinical samples. The ultimate goal of this proposal is to design systems and applications that are sufficiently robust and inexpensive to be used virtually anywhere, to address a wide variety of diseases. PROPOSED COMMERCIAL APPLICATIONS: 2.1 Billion people harbor a TB infection. UNICEF reports that tuberculosis poses a serious risk to Asia's sustained socioeconomic development: In a recent National Intelligence Estimate, the Central Intelligence Agency singled out drug-resistant TB - and especially its incidence among immigrants - as a potential threat to national security. Salomon and Murray report that world expenditure on TB therapy and diagnosis was $4.1 Billion (USD) in 1998. Diagnosis of TB worldwide is by sputum smear, with 50% accuracy. This new diagnostic is desperately needed.